Just run it through the firewall and under the carpet on the side where it won't get stepped on. And make sure it doesn't rub on anything as to wear a hole in the side of the insulation. About all I can really think of.
Hey man, i just got a 97 jetta, and from what i can tell, the panels under where the door sits when it's closed has tons of room, you should be able to run it under there, and then into the back, and then from there into the trunk. My back seats fold down so i can easily get the cables into the trunk, not sure about other jetta's, but that's how i'll be doing mine.